Anno genominis XX: 20 years of Arabidopsis genomics

Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.

The publication of the Arabidopsis genome sequence 20 years ago has had an enormous impact on the global plant science community.     

Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.     

Genome evolution in filamentous plant pathogens: why bigger can be better

Many species of fungi and oomycetes are plant pathogens of great economic importance. Over the past 7 years, the genomes of more than 30 of these filamentous plant pathogens have been sequenced, revealing remarkable diversity in genome size and architecture. Whereas the genomes of many parasites and bacterial symbionts have been reduced over time, the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansions. In these lineages, the genes encoding proteins involved in host interactions are frequently polymorphic and reside within repeat-rich regions of the genome. Here, we review the properties of these adaptable genome regions and the mechanisms underlying their plasticity, and we illustrate cases in which genome plasticity has contributed to the emergence of new virulence traits. We also discuss how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts.     

The role of plastids and assimilate transport system in the control of plant development

Phylogenetic and ontogenetic relationships between the plastids, cell endoplasmic reticulum, and plant transport communication have been reviewed. The initiating role of plastids (endosymbionts) in the origin of endoplasmic reticulum (buffer zone of endosymbiogenesis) has been shown, as well as a similar role of endoplasmic reticulum in the development of transport communication of xylem and phloem. Plastids, sugars and transport system for their distribution can be interpreted as leading sections in the mechanism of developmental control: gene expression of nuclear genome and genome of organelles, cell and tissue differentiation, and plant morphogenesis. The conflict between the bulk of plant genome and low percentage of its realization is explained as a result of limitation of the nuclear genome realization by plastid genome. The concept of development as applied to plant ontogenesis has been critically analyzed. The possibilities of the concept correction by with the help of symbiogenetic hypothesis are discussed.     

Genome size variations within Dasypyrum villosum: correlations with chromosomal traits, environmental factors and plant phenotypic characteristics and behaviour in reproduction

 Feulgen/DNA cytophotometric determinations carried out in the root meristem of seedlings showed that substantial quantitative alterations in the nuclear genome are present between and within 15 natural populations of Dasypyrum villosum in Italy. When the most variant values are considered, there is a 17.6% difference between the mean genome size of the populations, and a 66.2% difference between the genome size of individual plants within a population. A highly significant, positive correlation was found to exist between the genome size of D. villosum plants and the altitude of their stations, and differences in DNA contents between individual plants were greater in populations from mountain sites. Karyological analyses showed all chromosome pairs to differ largely in size between plants with differing DNA contents. A highly significant, positive correlation was found to exist between genome size and both the length of the chromosome complement at metaphase and the length and arm ratio of pair VII. Significant correlations were also found between DNA content and certain phenotypic characteristics of the plants. The mean genome size of the populations was negatively correlated with the mean leaf length and width. In contrast, the genome size of individual plants was positively correlated with the weight of the seed from which they originated and their flowering interval. A large range of genome sizes was found in the half-sib progeny of a plant having a relatively large genome. In contrast, in the half-sib progeny of a plant having a small genome, the genome sizes of the individual plants were less divergent and similar to that of the mother plant. All siblings from crosses between plants with differing genome sizes had similar DNA contents, which were intermediate between those of the parental plants, even if closer to the DNA content of the parent plant having the smaller genome size. Size polymorphism within pairs was never observed in plants obtained from these crosses or in half-sibs whose genome size differed from that of the mother plant. The intraspecific alterations observed in the nuclear genome and their effects on plant development and phenotype are briefly discussed as evolutionary factors which allow D. villosum populations to withstand different environmental conditions as well as the variability of conditions in a given environment. Received: 6 October 1997 / Accepted: 28 October 1997     

Journey through the past: 150 million years of plant genome evolution

The genome sequence of the plant model organism Arabidopsis thaliana was presented in December of the year 2000. Since then, the 125 Mb sequence has revealed many of its evolutionary secrets. Through comparative analyses with other plant genomes, we know that the genome of A. thaliana, or better that of its ancestors, has undergone at least three whole genome duplications during the last 120 or so million years. The first duplication seems to have occurred at the dawn of dicot evolution, while the later duplications probably occurred <70 million years ago (Ma). One of those younger genome-wide duplications might be linked to the K-T extinction. Following these duplication events, the ancestral A. thaliana genome was hugely rearranged and gene copies have been massively lost. During the last 10 million years of its evolution, almost half of its genome was lost due to hundreds of thousands of small deletions. Here, we reconstruct plant genome evolution from the early angiosperm ancestor to the current A. thaliana genome, covering about 150 million years of evolution characterized by gene and genome duplications, genome rearrangements and genome reduction.     

RNAi 在植物功能基因组中的应用

植物生物学后基因组时代的主要目标就是确定植物基因组中所有基因所具有的功能。解决这个问题的一个最直接的方法就是还原或者敲除某个在正常条件下其功能能表达出一定的可观察到的表型的特殊基因。对于这方面的研究,插入突变技术就是一个可用的工具,但是基因的随机性,致死敲除,无标记的突变体都大大地限制了这种技术的利用。RNm技术可以克服以上那些难题。它已经被广泛地应用在线虫的功能基因组上,并且所获得的有效资源还被广泛地用于植物功能基因组的分析。     

Evolution of plant mitochondrial genomes via substoichiometric intermediates

Comparison of the modern fertile maize mitochondrial genome (N) with an ancestral maize mitochondrial genome (RU) reveals a 12 kb duplication (containing the atpA gene) in the modern genome that is absent from the ancestor. Cloning, mapping, and sequencing of the relevant portions of the ancestral genome shows that this duplication probably arose via a three-stage recombination process involving substoichiometric intermediates. Comparison with analogous observations on yeast mitochondrial genomes suggests that this three-stage model of genome reorganization can be generally applied to plant mitochondrial genomes to explain both deletions and the creation of novel repeats, common features of plant mitochondrial genome evolution.     

LTR retrotransposons and flowering plant genome size: emergence of the increase/decrease model

Long Terminal Repeat (LTR) retrotransposons are ubiquitous components of plant genomes. Because of their copy-and-paste mode of transposition, these elements tend to increase their copy number while they are active. In addition, it is now well established that the differences in genome size observed in the plant kingdom are accompanied by variations in LTR retrotransposon content, suggesting that LTR retrotransposons might be important players in the evolution of plant genome size, along with polyploidy. The recent availability of large genomic sequences for many crop species has made it possible to examine in detail how LTR retrotransposons actually drive genomic changes in plants. In the present paper, we provide a review of the recent publications that have contributed to the knowledge of plant LTR retrotransposons, as structural components of the genomes, as well as from an evolutionary genomic perspective. These studies have shown that plant genomes undergo genome size increases through bursts of retrotransposition, while there is a counteracting process that tends to eliminate the transposed copies from the genomes. This process involves recombination mechanisms that occur either between the LTRs of the elements, leading to the formation of solo-LTRs, or between direct repeats anywhere in the sequence of the element, leading to internal deletions. All these studies have led to the emergence of a new model for plant genome evolution that takes into account both genome size increases (through retrotransposition) and decreases (through solo-LTR and deletion formation). In the conclusion, we discuss this new model and present the future prospects in the study of plant genome evolution in relation to the activity of transposable elements.     

Engineering Resistance Against Viruses in Field Crops Using CRISPR- Cas9

Food security is threatened by various biotic stresses that affect the growth and production of agricultural crops. Viral diseases have become a serious concern for crop plants as they incur huge yield losses. The enhancement of host resistance against plant viruses is a priority for the effective management of plant viral diseases. However, in the present context of the climate change scenario, plant viruses are rapidly evolving, resulting in the loss of the host resistance mechanism. Advances in genome editing techniques, such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9], have been recognized as promising tools for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simplicity, efficiency, and reproducibility. CRISPR-Cas9 based virus resistance in plants has been successfully achieved by gene targeting and cleaving the viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have described the CRISPR-Cas9 system, mechanism of plant immunity against viruses and highlighted the use of the CRISPR-Cas9 system to engineer virus resistance in plants. We also discussed prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.     

Expressed sequence tags: alternative or complement to whole genome sequences?

Over three million sequences from approximately 200 plant species have been deposited in the publicly available plant expressed sequence tag (EST) sequence databases. Many of the ESTs have been sequenced as an alternative to complete genome sequencing or as a substrate for cDNA array-based expression analyses. This creates a formidable resource from both biodiversity and gene-discovery standpoints. Bioinformatics-based sequence analysis tools have extended the scope of EST analysis into the fields of proteomics, marker development and genome annotation. Although EST collections are certainly no substitute for a whole genome scaffold, this "poor man's genome" resource forms the core foundations for various genome-scale experiments within the as yet unsequenceable plant genomes.     

Mechanisms and rates of genome expansion and contraction in flowering plants

Plant genomes are exceptional for their great variation in genome size, an outcome derived primarily from their frequent polyploid origins and from the amplification of retrotransposons. Although most studies of plant genome size variation have focused on developmental or physiological effects of nuclear DNA content that might influence plant fitness, more recent studies have begun to investigate possible mechanisms for plant genome expansion and contraction. Analyses of relatively neutral genome components, like transposable elements, have been particularly fruitful, largely due to the enormous growth in genomic sequence information from many different plant species. Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.     

高等植物基因组测序回顾与展望

全基因组序列测定为揭示植物重要性状形成的分子和遗传机制提供了强大工具,基因组学研究正开始指引着农作物新品种培育向定向化和精确化转变.在新一代测序技术的带动下,植物全基因组测序的热潮已经到来.对迄今开展的高等植物基因组测序工作进行简要回顾,并对未来的研究热点进行展望.     

Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model

The interaction of pathogens with their hosts creates strong reciprocal selection pressures. Pathogens often deploy an arsenal of small proteins called effectors that manipulate the plant immune system and promote disease. In the post-genomics era, a major interest has been to understand what shapes the localization of effector genes in pathogen genomes. The two-speed genome model originated with the discovery of repeat-rich and gene-sparse genome compartments with an over-representation of effector-like genes in a subset of plant pathogens. These highly polymorphic genome compartments are thought to create unique niches for effector genes and facilitate rapid adaptation. Research over the past decade has revealed a number of twists to the two-speed genome model and raised questions about the universality among plant pathogens. Here, we critically review the foundations of the two-speed model by presenting recent work on epigenetics, transposable element dynamics, and population genetics. Numerous examples have demonstrated that the location of effector genes in rapidly evolving compartments has created key adaptations. However, recent evidence suggests that the two-speed genome is unlikely to have evolved to specifically benefit the plant pathogen lifestyle. We propose that fundamental drivers of eukaryotic genome evolution have shaped both pathogen and non-pathogen genomes alike. An evolutionary genomics perspective on the two-speed genome model will open up fruitful new research avenues.     

Chloroplast genome sequences from total DNA for plant identification

Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost‐effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are non‐trivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost‐effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single‐locus DNA barcode for plants.     

植物基因组大小进化的研究进展

不同的真核生物之间基因组大小差异很大, 并与生物体复杂性不相关, 在基因组中存在大量的非编码DNA序列是造成这种差异的主要原因, 特别是转座子序列。文章综述了植物基因组大小差异以及引起这种差异的主要进化动力的最新研究进展。植物基因组多倍化和转座子积累是导致基因组增大的主要动力, 而同源不平等重组和非正规重组则是驱动基因组DNA丢失的潜在动力, 以制约基因组无限制地增大。文中还讨论了植物基因组大小进化方向, 即总体趋势是朝着增大的方向进化, 某些删除机制主要是削弱这种增大作用但不能逆转。     

The Role of Plastids and Assimilate Transport System in the Control of Plant Development

Phylogenetic and ontogenetic relationships between the plastids, cell endoplasmic reticulum, and plant transport communication have been reviewed. The initiating role of plastids (endosymbionts) in the origin of endoplasmic reticulum (buffer zone of endosymbiogenesis) has been shown, as well as a similar role of endoplasmic reticulum in the development of transport communication of xylem and phloem. Plastids, sugars and transport system for their distribution can be interpreted as leading sections in the mechanism of developmental control: gene expression of nuclear genome and genome of organelles, cell and tissue differentiation, and plant morphogenesis. The conflict between the bulk of plant genome and low percentage of its realization is explained as a result of limitation of the nuclear genome realization by plastid genome. The concept of development as applied to plant ontogenesis has been critically analyzed. The possibilities of the concept correction by with the help of symbiogenetic hypothesis are discussed.__________Translated from Ontogenez, Vol. 36, No. 3, 2005, pp. 165–181.Original Russian Text Copyright © 2005 by Gamalei.     

Weeding out the genes: the Arabidopsis genome project

The Arabidopsis genome sequence is scheduled for completion at the end of this year (December 2000). It will be the first higher plant genome to be sequenced, and will allow a detailed comparison with bacterial, yeast and animal genomes. Already, two of the five chromosomes have been sequenced, and we have had our first glimpse of higher eukaryotic centromeres, and the structure of heterochromatin. The implications for understanding plant gene function, genome structure and genome organization are profound. In this review, the lessons learned for future genome projects are reviewed as well as a summary of the initial findings in Arabidopsis. Electronic Publication     

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

Background

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.

Methodology/Principal Findings

We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.

Conclusion

The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.